Mr Partridge has nearly 900 cattle on his farm
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Defra will have to rethink how it compensates farmers whose pedigree cattle are culled because of bovine TB, a High Court judge has ruled.
It follows a Devon farmer's judicial challenge against the "unfair and unequal" way compensation is paid.
David Partridge, from Ennerleigh Farm, near Tiverton, argued Defra's scheme left farmers of well-bred cattle seriously under-compensated.
Lord Justice Stanley Burnton gave Defra permission to challenge the decision.
Mr Partridge told BBC News he was pleased with the ruling.
'Devastating blow'
"We'll need to wait and see if Defra decide to challenge it," he said.
In the ruling, the judge said it was "perverse" of Defra to claim the value of pedigree cattle culled under the policy was being "realistically or fairly determined" before compensation is paid.
Upholding Mr Partridge's judicial review challenge, the judge said: "The Secretary of State has not satisfied me that reasonably reliable means of fairly compensating farmers with high value cattle at reasonable expense is impossible or impractical to achieve".
Mr Patridge's barrister, Hugh Mercer QC, had told the judge the current compensation scheme amounted to a "disincentive" both to careful cattle breeding and the introduction of bio-security methods to reduce the impact of TB on the UK's dairy and beef herds.
Mr Partridge said his cows were worth £3,000 each on the open market
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He told the court Ennerleigh Farm was in one of the worst "hot spots" for bovine TB and over recent years more than 100 of Mr Partridge's cattle had been compulsorily slaughtered after testing positive for the disease.
Mr Mercer said it was a "devastating" blow for the 700-acre farm, which has almost 900 cattle and which prides itself on the breeding and quality of its stock.
Mr Partridge's challenge was targeted at Defra's decision in March 2006 to pay £8,726 compensation for eight of his prize cows slaughtered under the scheme.
The 60-year-old farmer said the cows would have fetched an average of more than £3,000 each on the open market and his compensation should have been more than £24,000.
His pedigree Holsteins were monitored regularly by a vet and produced far more milk than average.
Mr Partridge told the judge Defra's compensation appeared to act as a counter-incentive to providing the stock quality and adopting best practice in animal husbandry.
Additional compensation
After the ruling, the judge said he was granting Defra permission to challenge his decision because he recognised the widespread importance of the case to the farming industry.
Mr Partridge said he would be speaking to his solicitor with regard to claiming additional compensation.
No-one from Defra has been available to comment.
The National Farmers' Union (NFU) has welcomed the High Court ruling.
In a statement, NFU president Peter Kendall said: "The NFU has always argued the way Defra implemented table values was grossly unfair to producers of high value, quality animals which are slaughtered for TB control purposes.
"We are pleased that a court has taken the same view."
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